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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ), 'gf_id' => 'HOM05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001127' ), 'data_identifier' => 'HOM05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '547', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p35540' => 'bna', 'A04p30640' => 'bna', 'A04p30690' => 'bna', 'A05p08620' => 'bna', 'A05p40350' => 'bna', 'A08p08880' => 'bna', 'A09p19460' => 'bna', 'A09p48040' => 'bna', 'Aa31LG11G7550' => 'aar', 'Aa31LG5G18440' => 'aar', 'Aa31LG5G22610' => 'aar', 'Aa31sc33G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1190' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2797' => 'aag', 'Actinidia03010' => 'ach', 'Actinidia03011' => 'ach', 'Actinidia09766' => 'ach', 'Actinidia10785' => 'ach', 'Actinidia13723' => 'ach', 'Actinidia13843' => 'ach', 'Actinidia19725' => 'ach', 'Actinidia25651' => 'ach', 'Actinidia29193' => 'ach', 'Actinidia33531' => 'ach', 'Actinidia38233' => 'ach', 'Ah.01g001770' => 'amhyb', 'Ah.10g033120' => 'amhyb', 'Ah.14g082950' => 'amhyb', 'Ah.15g092000' => 'amhyb', 'AL3G19260' => 'aly', 'AL4G33670' => 'aly', 'AL4G36590' => 'aly', 'AL5G26010' => 'aly', 'AL5G26020' => 'aly', 'AL5G36140' => 'aly', 'Aqoxy1G04067' => 'aox', 'Aqoxy2G01897' => 'aox', 'Aqoxy4G03131' => 'aox', 'Aqoxy4G03138' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N89KK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3J5MDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AD7TE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.502G41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DZY9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SBX1U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B3B375' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D60R3M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DFL4HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F92JFJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP1DZ8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7SU3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WAX40B' => 'arhy', 'AT2G37290' => 'ath', 'AT2G39280' => 'ath', 'AT3G07890' => 'ath', 'AT3G55020' => 'ath', 'ATR0594G169' => 'atr', 'ATR0624G040' => 'atr', 'Atru.chr12.606' => 'acertr', 'Atru.chr6.3316' => 'acertr', 'Atru.chr6.3321' => 'acertr', 'Atru.chr8.2520' => 'acertr', 'Atru.chr8.2521' => 'acertr', 'Atru.chr8.2522' => 'acertr', 'Atru.chr8.2523' => 'acertr', 'AUR62015097' => 'cqu', 'AUR62017557' => 'cqu', 'AUR62035999' => 'cqu', 'AUR62041621' => 'cqu', 'BcaB02g09291' => 'bca', 'BcaB04g21266' => 'bca', 'BcaB06g26276' => 'bca', 'BcaB06g29072' => 'bca', 'BcaB06g29074' => 'bca', 'BcaB07g33766' => 'bca', 'BcaC02g07333' => 'bca', 'BcaC02g07336' => 'bca', 'BcaC02g07416' => 'bca', 'BcaC02g11849' => 'bca', 'BcaC05g29579' => 'bca', 'BcaC07g38641' => 'bca', 'BcaC07g39820' => 'bca', 'BcaC09g47956' => 'bca', 'BcaC09g47960' => 'bca', 'BcaNung04654' => 'bca', 'BcaNung05996' => 'bca', 'BolC1t05520H' => 'bol', 'BolC3t16587H' => 'bol', 'BolC4t22664H' => 'bol', 'BolC4t28215H' => 'bol', 'BolC4t28303H' => 'bol', 'BolC4t28304H' => 'bol', 'BolC4t28316H' => 'bol', 'BolC5t34600H' => 'bol', 'BolC8t50633H' => 'bol', 'BraA01t04354Z' => 'bra', 'BraA03t12729Z' => 'bra', 'BraA04t18524Z' => 'bra', 'BraA04t18528Z' => 'bra', 'BraA05t19830Z' => 'bra', 'BraA09t40257Z' => 'bra', 'C03p43180' => 'bna', 'C03p54820' => 'bna', 'C04p10710' => 'bna', 'C04p67150' => 'bna', 'C04p68100' => 'bna', 'C05p59440' => 'bna', 'C08p30260' => 'bna', 'CAN.G186.32' => 'can', 'CAN.G283.4' => 'can', 'CAN.G350.54' => 'can', 'CAN.G784.6' => 'can', 'CANSAT56G3216' => 'cansat', 'CANSAT64G1437' => 'cansat', 'CANSAT80G0329' => 'cansat', 'CARHR082620' => 'chi', 'CARHR132300' => 'chi', 'CARHR134030' => 'chi', 'CARHR149210' => 'chi', 'CARHR165040' => 'chi', 'Carub.0003s0747' => 'cru', 'Carub.0004s1920' => 'cru', 'Carub.0004s2133' => 'cru', 'Carub.0005s2165' => 'cru', 'Ca_02303_v3' => 'car', 'Ca_06477_v3' => 'car', 'Ca_11384_v3' => 'car', 'Ca_11386_v3' => 'car', 'CBR_g29911' => 'cbr', 'CBR_g38652' => 'cbr', 'CBR_g38658' => 'cbr', 'Cc00_g04680' => 'ccan', 'Cc06_g03380' => 'ccan', 'Cc09_g02300' => 'ccan', 'CDE02G0072' => 'cde', 'CDE04G0788' => 'cde', 'CDE04G1225' => 'cde', 'CDE04G1624' => 'cde', 'CDE07G2002' => 'cde', 'CDE09G1289' => 'cde', 'Cfa001570' => 'cfa', 'Cfa014281' => 'cfa', 'Cfa017482' => 'cfa', 'Cfa025559' => 'cfa', 'Cfa026169' => 'cfa', 'Ciclev10011283m.g' => 'ccl', 'Ciclev10015500m.g' => 'ccl', 'Ciclev10030687m.g' => 'ccl', 'CiPaw.01G278600' => 'cil', 'CiPaw.02G177900' => 'cil', 'CiPaw.03G276000' => 'cil', 'CiPaw.04G193800' => 'cil', 'CiPaw.09G184300' => 'cil', 'ClCG02G009550' => 'cla', 'ClCG02G013750' => 'cla', 'ClCG10G020690' => 'cla', 'COL.COLO4_06786' => 'col', 'COL.COLO4_10298' => 'col', 'COL.COLO4_35989' => 'col', 'Cpa.g.sc1.293' => 'cpa', 'Cpa.g.sc114.59' => 'cpa', 'Cpa.g.sc132.75' => 'cpa', 'Cre02.g077700' => 'cre', 'Cre07.g315350' => 'cre', 'Cre09.g396846' => 'cre', 'Cre10.g459800' => 'cre', 'Cre10.g461400' => 'cre', 'Cre17.g737050' => 'cre', 'CsaV3_2G034270' => 'csa', 'CsaV3_3G035400' => 'csa', 'CsaV3_5G006420' => 'csa', 'CSS0003419' => 'camsi', 'CSS0013454' => 'camsi', 'CSS0014447' => 'camsi', 'CSS0018774' => 'camsi', 'CSS0019401' => 'camsi', 'CSS0030501' => 'camsi', 'CSS0036171' => 'camsi', 'DCAR_006486' => 'dca', 'DCAR_009270' => 'dca', 'DCAR_012911' => 'dca', 'DCAR_015257' => 'dca', 'DCAR_019723' => 'dca', 'DCAR_021119' => 'dca', 'Dinv05853' => 'din', 'Dinv07829' => 'din', 'Dinv08687' => 'din', 'Dinv11997' => 'din', 'Dinv25935' => 'din', 'Dinv31380' => 'din', 'Dinv35689' => 'din', 'Dinv35690' => 'din', 'Duzib093G0050' => 'dzi', 'Duzib106G1380' => 'dzi', 'Duzib106G1592' => 'dzi', 'Duzib114G0575' => 'dzi', 'Duzib128G1061' => 'dzi', 'Duzib133G0790' => 'dzi', 'Duzib138G0261' => 'dzi', 'Duzib211G0460' => 'dzi', 'ECA232G1988' => 'eca', 'ECA234G4445' => 'eca', 'ECA238G3032' => 'eca', 'ECA240G0316' => 'eca', 'ECA248G3496' => 'eca', 'EL10Ac2g03527' => 'bvu', 'EL10Ac3g05660' => 'bvu', 'EL10Ac7g17259' => 'bvu', 'EL10Ac7g17260' => 'bvu', 'Eucgr.A01077' => 'egr', 'Eucgr.A01196' => 'egr', 'Eucgr.J01140' => 'egr', 'FAN01G0130' => 'fan', 'FAN01G2826' => 'fan', 'FAN02G0053' => 'fan', 'FAN02G3319' => 'fan', 'FAN03G3433' => 'fan', 'FAN05G1989' => 'fan', 'FAN05G2345' => 'fan', 'FAN06G2619' => 'fan', 'FAN06G4441' => 'fan', 'FAN09G2613' => 'fan', 'FAN09G3206' => 'fan', 'FAN10G1953' => 'fan', 'FAN14G1132' => 'fan', 'FAN14G2849' => 'fan', 'FAN14G3825' => 'fan', 'FAN14G5288' => 'fan', 'FvH4_6g15020' => 'fve', 'FvH4_6g41560' => 'fve', 'FvH4_7g20590' => 'fve', 'Glyma.02G308000' => 'gma', 'Glyma.10G047800' => 'gma', 'Glyma.10G294700' => 'gma', 'Glyma.13G135700' => 'gma', 'Glyma.14G005100' => 'gma', 'Glyma.20G244400' => 'gma', 'Gohir.A01G218050' => 'ghi', 'Gohir.A02G086302' => 'ghi', 'Gohir.A04G077333' => 'ghi', 'Gohir.A04G077366' => 'ghi', 'Gohir.A05G299100' => 'ghi', 'Gohir.A07G086000' => 'ghi', 'Gohir.A07G177200' => 'ghi', 'Gohir.A07G189100' => 'ghi', 'Gohir.A10G208300' => 'ghi', 'Gohir.A13G021100' => 'ghi', 'Gohir.D01G206933' => 'ghi', 'Gohir.D04G112260' => 'ghi', 'Gohir.D04G112833' => 'ghi', 'Gohir.D04G116500' => 'ghi', 'Gohir.D04G116533' => 'ghi', 'Gohir.D05G298800' => 'ghi', 'Gohir.D05G341000' => 'ghi', 'Gohir.D06G074550' => 'ghi', 'Gohir.D07G091100' => 'ghi', 'Gohir.D07G174000' => 'ghi', 'Gohir.D07G195480' => 'ghi', 'Gohir.D10G216600' => 'ghi', 'Gohir.D12G188368' => 'ghi', 'Gohir.D13G021600' => 'ghi', 'Gohir.D13G021800' => 'ghi', 'Gorai.001G097600' => 'gra', 'Gorai.001G194500' => 'gra', 'Gorai.001G198200' => 'gra', 'Gorai.001G218800' => 'gra', 'Gorai.002G251900' => 'gra', 'Gorai.008G202200' => 'gra', 'Gorai.009G316000' => 'gra', 'Gorai.009G416600' => 'gra', 'Gorai.009G421300' => 'gra', 'Gorai.009G421400' => 'gra', 'Gorai.011G242200' => 'gra', 'Gorai.012G120800' => 'gra', 'Gorai.013G024400' => 'gra', 'Gorai.013G024600' => 'gra', 'GSVIVG01025561001' => 'vvi', 'GSVIVG01025565001' => 'vvi', 'GSVIVG01030412001' => 'vvi', 'GSVIVG01032641001' => 'vvi', 'HanXRQChr01g0004061' => 'han', 'HanXRQChr01g0027011' => 'han', 'HanXRQChr02g0038481' => 'han', 'HanXRQChr05g0153051' => 'han', 'HanXRQChr07g0200951' => 'han', 'HanXRQChr09g0243691' => 'han', 'HanXRQChr10g0306321' => 'han', 'HanXRQChr11g0349571' => 'han', 'HanXRQChr12g0381721' => 'han', 'HanXRQChr14g0460831' => 'han', 'HanXRQChr15g0496851' => 'han', 'HanXRQChr17g0556401' => 'han', 'Haze_12726' => 'cav', 'Haze_16959' => 'cav', 'Haze_20676' => 'cav', 'Hma1.2p1_0111F.1_g053610' => 'hma', 'Hma1.2p1_0133F.1_g060960' => 'hma', 'Hma1.2p1_0207F.1_g088050' => 'hma', 'Hma1.2p1_0348F.1_g131810' => 'hma', 'Hma1.2p1_1158F.1_g262380' => 'hma', 'HPP92_007481' => 'vpl', 'HPP92_019799' => 'vpl', 'HPP92_025065' => 'vpl', 'HPP92_025069' => 'vpl', 'HPP92_025070' => 'vpl', 'HPP92_025080' => 'vpl', 'HPP92_025081' => 'vpl', 'HPP92_025082' => 'vpl', 'Hund12065' => 'sun', 'Hund19287' => 'sun', 'Hund22440' => 'sun', 'Hund24165' => 'sun', 'Lalb_Chr02g0144201' => 'lal', 'Lalb_Chr02g0144211' => 'lal', 'Lalb_Chr02g0153551' => 'lal', 'Lalb_Chr04g0247141' => 'lal', 'Lalb_Chr06g0164381' => 'lal', 'Lalb_Chr10g0107631' => 'lal', 'Lalb_Chr17g0349271' => 'lal', 'Lalb_Chr21g0307551' => 'lal', 'Lj1A927T61' => 'lonja', 'Lj1C928T14' => 'lonja', 'Lj2A105G63' => 'lonja', 'Lj2A105G64' => 'lonja', 'Lj2P105G28' => 'lonja', 'Lj5g0015647' => 'lja', 'Lj5g0024475' => 'lja', 'Lj8A132T53' => 'lonja', 'LjContig00081g0006770' => 'lja', 'Lsat_1_v5_gn_1_53421' => 'lsa', 'Lsat_1_v5_gn_2_115380' => 'lsa', 'Lsat_1_v5_gn_5_124761' => 'lsa', 'Lsat_1_v5_gn_5_55941' => 'lsa', 'Lsat_1_v5_gn_9_105400' => 'lsa', 'Lsat_1_v5_gn_9_66141' => 'lsa', 'Manes.07G105500' => 'mes', 'Manes.08G001400' => 'mes', 'Manes.10G040200' => 'mes', 'Manes.12G060701' => 'mes', 'Manes.13G063955' => 'mes', 'Mapoly0028s0025' => 'mpo', 'Mapoly0032s0079' => 'mpo', 'MBI14_g14542_MAGBIO' => 'mbi', 'MBI14_g45856_MAGBIO' => 'mbi', 'MCO07G442' => 'mco', 'MCO08G275' => 'mco', 'MCO10G206' => 'mco', 'MCO11G755' => 'mco', 'MD01G1114800' => 'mdo', 'MD04G1112400' => 'mdo', 'MD07G1182800' => 'mdo', 'MD09G1118900' => 'mdo', 'MD12G1129300' => 'mdo', 'MD17G1109700' => 'mdo', 'Medtr1g067150' => 'mtr', 'Medtr1g116310' => 'mtr', 'Medtr5g098140' => 'mtr', 'MELO3C004919.2' => 'cme', 'MELO3C011716.2' => 'cme', 'MELO3C013431.2' => 'cme', 'MELO3C019359.2' => 'cme', 'MELO3C031022.2' => 'cme', 'Migut.F01786' => 'egut', 'Migut.F02011' => 'egut', 'Migut.H01294' => 'egut', 'Migut.L01649' => 'egut', 'Migut.M00008' => 'egut', 'MSTRG.14934' => 'ama', 'MSTRG.8157' => 'ama', 'MSTRG.9190' => 'ama', 'Nitab4.5_0000130g0190' => 'nta', 'Nitab4.5_0000575g0050' => 'nta', 'Nitab4.5_0000622g0220' => 'nta', 'Nitab4.5_0000691g0200' => 'nta', 'Nitab4.5_0000848g0020' => 'nta', 'Nitab4.5_0002127g0020' => 'nta', 'Nitab4.5_0004104g0040' => 'nta', 'Nitab4.5_0004432g0010' => 'nta', 'Nitab4.5_0007644g0020' => 'nta', 'Nitab4.5_0008746g0040' => 'nta', 'Nn1g03312' => 'nnu', 'Nn1g07381' => 'nnu', 'Nn2g10591' => 'nnu', 'Nn2g12948' => 'nnu', 'Oeu017249.1' => 'oeu', 'Oeu029109.1' => 'oeu', 'Oeu029810.1' => 'oeu', 'Oeu046888.2' => 'oeu', 'Oeu057251.2' => 'oeu', 'Os01g0835000' => 'osa', 'Os03g0283800' => 'osa', 'Os05g0465100' => 'osa', 'Os08g0337700' => 'osa', 'Peaxi162Scf00047g01920' => 'pax', 'Peaxi162Scf00170g00052' => 'pax', 'Peaxi162Scf00195g00836' => 'pax', 'Peaxi162Scf00543g00420' => 'pax', 'Peaxi162Scf01333g00145' => 'pax', 'PGR004G2892' => 'pgr', 'PGR042G0445' => 'pgr', 'PGR044G2328' => 'pgr', 'PGSC0003DMG400006427' => 'stu', 'PGSC0003DMG400013895' => 'stu', 'PGSC0003DMG401027896' => 'stu', 'PGSC0003DMG403027896' => 'stu', 'Phvul.007G005500' => 'pvu', 'Phvul.007G162150' => 'pvu', 'Phvul.008G287900' => 'pvu', 'Potri.002G218100' => 'ptr', 'Potri.006G133400' => 'ptr', 'Potri.008G046600' => 'ptr', 'Potri.010G215000' => 'ptr', 'Potri.014G163400' => 'ptr', 'Pp3c11_21180' => 'ppa', 'Pp3c18_4400' => 'ppa', 'Pp3c19_14290' => 'ppa', 'Pp3c19_14410' => 'ppa', 'Pp3c21_14960' => 'ppa', 'Pp3c5_25800' => 'ppa', 'PRCOL_00002434' => 'pco', 'PRCOL_00006223' => 'pco', 'PRCOL_00006443' => 'pco', 'Prupe.2G221500' => 'ppe', 'Prupe.3G205400' => 'ppe', 'Prupe.6G244600' => 'ppe', 'Psat1g003720' => 'psa', 'Psat2g003600' => 'psa', 'Psat6g125000' => 'psa', 'Psat6g144680' => 'psa', 'Psat6g240240' => 'psa', 'Psat6g240280' => 'psa', 'Psat7g069560' => 'psa', 'PSO210G7478' => 'pso', 'PSO302G0292' => 'pso', 'PSO339G3179' => 'pso', 'PSO384G1853' => 'pso', 'PSO384G4700' => 'pso', 'PSO713G0001' => 'pso', 'QL07p045698' => 'qlo', 'QL08p029678' => 'qlo', 'QL08p057343' => 'qlo', 'RcHm_v2.0_Chr1g0364631' => 'rch', 'RcHm_v2.0_Chr2g0094461' => 'rch', 'RcHm_v2.0_Chr2g0157241' => 'rch', 'RcHm_v2.0_Chr3g0468201' => 'rch', 'Rhsim03G0121200' => 'rsi', 'Rhsim04G0046000' => 'rsi', 'Rhsim06G0171200' => 'rsi', 'RhsimUnG0119800' => 'rsi', 'RhsimUnG0119900' => 'rsi', 'Sabra02G0170400' => 'sbr', 'Sabra06G0104900' => 'sbr', 'Sabra08G0032900' => 'sbr', 'Sabra10G0166100' => 'sbr', 'Sabra14G0124700' => 'sbr', 'SalBow4G2749' => 'sbo', 'SalBow7G4161' => 'sbo', 'Sc01g0003680' => 'sci', 'Sc09g0007120' => 'sci', 'Sc20g0003830' => 'sci', 'Sed0006111' => 'sed', 'Sed0010697' => 'sed', 'Sed0016528' => 'sed', 'Sed0017503' => 'sed', 'Sed0018007' => 'sed', 'Sed0022503' => 'sed', 'Sed0026750' => 'sed', 'SEGI_35068' => 'sgi', 'SEGI_41029' => 'sgi', 'SGA_v2.0_scaffold329G48854' => 'sas', 'SGA_v2.0_scaffold49G18419' => 'sas', 'SGA_v2.0_scaffold540G52805' => 'sas', 'SGA_v2.0_scaffold62G21440' => 'sas', 'SGA_v2.0_scaffold71G24031' => 'sas', 'SGA_v2.0_scaffold94G28652' => 'sas', 'SHI28200' => 'shi', 'SMO119G0184' => 'smo', 'SMO203G0129' => 'smo', 'SMO364G0507' => 'smo', 'Solyc04g009560.3' => 'sly', 'Solyc07g049580.3' => 'sly', 'Solyc09g007160.4' => 'sly', 'Solyc12g005930.2' => 'sly', 'Sopen00g010770' => 'spe', 'Sopen04g004720' => 'spe', 'Sopen04g019650' => 'spe', 'Sopen04g019660' => 'spe', 'Sopen07g024980' => 'spe', 'Sopen09g002030' => 'spe', 'Sopen12g001880' => 'spe', 'Sp3g06810' => 'spa', 'Sp4g19610' => 'spa', 'Sp4g21600' => 'spa', 'Sp5g07400' => 'spa', 'SpUn0018_0070' => 'spa', 'TAR369G0283' => 'tar', 'TAR369G1035' => 'tar', 'TAR623G0446' => 'tar', 'TAR624G0192' => 'tar', 'TAR626G1600' => 'tar', 'TAR627G0952' => 'tar', 'TAR628G0918' => 'tar', 'TAR636G0771' => 'tar', 'TAR636G0989' => 'tar', 'TAR636G1651' => 'tar', 'THA.LOC104806517' => 'tha', 'THA.LOC104809868' => 'tha', 'THA.LOC104809989' => 'tha', 'THA.LOC104819052' => 'tha', 'THA.LOC104824244' => 'tha', 'Thecc.01G186500' => 'tca', 'Thecc.05G051300' => 'tca', 'Thecc.10G064300' => 'tca', 'Thhalv10010127m.g' => 'esa', 'Thhalv10016235m.g' => 'esa', 'Thhalv10017641m.g' => 'esa', 'Thhalv10020959m.g' => 'esa', 'TPR.G10432' => 'tpr', 'TPR.G15072' => 'tpr', 'TPR.G18802' => 'tpr', 'TPR.G35658' => 'tpr', 'TPR.G4854' => 'tpr', 'TWI15G1084' => 'twi', 'TWI18G1165' => 'twi', 'TWI53G1923' => 'twi', 'TWI75G1692' => 'twi', 'unitig_52.g17314' => 'ugi', 'unitig_62.g23951' => 'ugi', 'unitig_899.g15224' => 'ugi', 'vmacro07100' => 'vma', 'vmacro07149' => 'vma', 'vmacro09378' => 'vma', 'vmacro12135' => 'vma', 'vmacro20076' => 'vma', 'VMungo0647G2114' => 'vmu', 'VMungo0720G1490' => 'vmu', 'VMungo0720G2317' => 'vmu', 'VMungo0720G2346' => 'vmu', 'Zm00001eb013000' => 'zma', 'Zm00001eb095040' => 'zma', 'Zm00001eb148790' => 'zma', 'Zm00001eb176770' => 'zma', 'Zm00001eb289920' => 'zma', 'Zm00001eb351610' => 'zma', 'Zm00001eb354500' => 'zma', 'Zm00001eb397250' => 'zma', 'Zm00001eb429420' => 'zma' ) $gf_id = 'HOM05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001127' ) $data_identifier = 'HOM05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 25, 'gra' => (int) 14, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 3, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 10, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429420' $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